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Iron in PDB 3etr: Crystal Structure of Xanthine Oxidase in Complex with Lumazine

Protein crystallography data

The structure of Crystal Structure of Xanthine Oxidase in Complex with Lumazine, PDB code: 3etr was solved by J.M.Pauff, H.Cao, R.Hille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 133.190, 73.491, 146.505, 90.00, 98.68, 90.00
R / Rfree (%) 19.7 / 26.7

Other elements in 3etr:

The structure of Crystal Structure of Xanthine Oxidase in Complex with Lumazine also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine (pdb code 3etr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine, PDB code: 3etr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3etr

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Iron binding site 1 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:17.0
occ:1.00
 FE1 A:FES601 0.0 17.0 1.0
S2 A:FES601 2.2 16.8 1.0
S1 A:FES601 2.2 15.9 1.0
SG A:CYS113 2.3 16.3 1.0
SG A:CYS150 2.5 22.7 1.0
FE2 A:FES601 2.7 17.6 1.0
CB A:CYS150 3.3 17.6 1.0
CB A:CYS113 3.4 15.4 1.0
N A:CYS113 3.6 17.3 1.0
O C:HOH1346 3.6 17.2 1.0
N A:GLY114 3.9 14.9 1.0
CA A:CYS113 3.9 15.7 1.0
N A:CYS150 4.1 16.7 1.0
C A:CYS113 4.3 15.8 1.0
CA A:CYS150 4.3 18.9 1.0
N A:PHE115 4.4 13.5 1.0
SG A:CYS148 4.4 16.1 1.0
SG A:CYS116 4.6 16.7 1.0
C A:GLN112 4.7 18.2 1.0
N A:ARG149 4.7 16.4 1.0
CA A:GLY114 4.8 14.2 1.0
CB A:GLN112 4.8 18.3 1.0
N A:CYS116 4.9 14.7 1.0

Iron binding site 2 out of 8 in 3etr

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Iron binding site 2 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:17.6
occ:1.00
 FE2 A:FES601 0.0 17.6 1.0
S2 A:FES601 2.2 16.8 1.0
S1 A:FES601 2.2 15.9 1.0
SG A:CYS116 2.3 16.7 1.0
SG A:CYS148 2.3 16.1 1.0
FE1 A:FES601 2.7 17.0 1.0
CB A:CYS116 3.3 15.4 1.0
CB A:CYS148 3.3 15.8 1.0
CA A:CYS148 3.6 16.0 1.0
O A:HOH613 4.0 9.9 1.0
N A:ARG149 4.1 16.4 1.0
N A:CYS150 4.3 16.7 1.0
N A:CYS116 4.3 14.7 1.0
C A:CYS148 4.3 15.8 1.0
CB A:CYS150 4.3 17.6 1.0
CA A:CYS116 4.4 15.4 1.0
SG A:CYS150 4.6 22.7 1.0
SG A:CYS113 4.8 16.3 1.0
CG2 A:THR151 4.8 15.8 1.0
CA A:CYS150 4.9 18.9 1.0
N A:CYS148 4.9 17.0 1.0
O A:LEU147 4.9 17.6 1.0
C A:CYS116 5.0 15.9 1.0

Iron binding site 3 out of 8 in 3etr

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Iron binding site 3 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:15.4
occ:1.00
 FE1 A:FES602 0.0 15.4 1.0
S1 A:FES602 2.2 16.3 1.0
S2 A:FES602 2.2 16.8 1.0
SG A:CYS73 2.2 16.0 1.0
SG A:CYS51 2.3 12.6 1.0
FE2 A:FES602 2.8 13.7 1.0
CB A:CYS73 3.3 15.1 1.0
CB A:CYS51 3.3 11.7 1.0
CB A:ASN71 4.2 13.0 1.0
N A:CYS73 4.2 16.2 1.0
N A:CYS51 4.2 13.1 1.0
OD1 A:ASN71 4.3 16.1 1.0
N A:GLY46 4.3 15.0 1.0
CA A:CYS73 4.4 15.2 1.0
CG A:ASN71 4.4 14.1 1.0
CA A:CYS51 4.4 14.0 1.0
N A:GLY44 4.4 12.2 1.0
SG A:CYS43 4.5 14.2 1.0
CA A:GLY46 4.5 15.8 1.0
CA A:GLY44 4.7 12.7 1.0
SG A:CYS48 4.8 13.4 1.0
CA A:ASN71 4.8 14.7 1.0
N A:GLU45 4.8 14.9 1.0
N A:GLY49 4.9 13.6 1.0
N A:ALA50 5.0 12.3 1.0

Iron binding site 4 out of 8 in 3etr

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Iron binding site 4 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:13.7
occ:1.00
 FE2 A:FES602 0.0 13.7 1.0
S1 A:FES602 2.2 16.3 1.0
S2 A:FES602 2.3 16.8 1.0
SG A:CYS48 2.4 13.4 1.0
SG A:CYS43 2.4 14.2 1.0
FE1 A:FES602 2.8 15.4 1.0
CB A:CYS43 3.5 10.7 1.0
CB A:CYS48 3.5 14.5 1.0
N A:CYS48 3.6 16.2 1.0
N A:CYS43 3.6 12.5 1.0
N A:GLY44 3.8 12.2 1.0
N A:GLY49 3.9 13.6 1.0
CA A:CYS43 3.9 11.7 1.0
CA A:CYS48 3.9 14.1 1.0
C A:GLY42 4.1 12.9 1.0
C A:CYS48 4.2 13.8 1.0
N A:GLY42 4.3 13.9 1.0
C A:CYS43 4.3 12.9 1.0
CA A:GLY42 4.3 12.9 1.0
N A:ALA50 4.4 12.3 1.0
N A:GLY47 4.4 17.3 1.0
N A:GLY46 4.4 15.0 1.0
SG A:CYS73 4.5 16.0 1.0
N A:GLU45 4.6 14.9 1.0
SG A:CYS51 4.7 12.6 1.0
C A:GLY47 4.7 18.5 1.0
CA A:GLY49 4.8 13.3 1.0
C A:GLY46 4.8 16.2 1.0
CA A:GLY46 4.9 15.8 1.0
CA A:GLY44 4.9 12.7 1.0
O A:GLY42 5.0 12.8 1.0

Iron binding site 5 out of 8 in 3etr

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Iron binding site 5 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe601

b:21.9
occ:1.00
 FE1 L:FES601 0.0 21.9 1.0
S1 L:FES601 2.2 23.1 1.0
S2 L:FES601 2.2 23.8 1.0
SG L:CYS150 2.4 19.8 1.0
SG L:CYS113 2.5 21.2 1.0
FE2 L:FES601 2.7 22.4 1.0
CB L:CYS150 3.2 20.0 1.0
CB L:CYS113 3.5 19.1 1.0
N L:CYS113 3.6 20.6 1.0
O N:HOH1339 3.8 15.9 1.0
N L:GLY114 3.9 17.6 1.0
CA L:CYS113 4.0 19.9 1.0
N L:CYS150 4.0 18.6 1.0
CA L:CYS150 4.2 20.3 1.0
C L:CYS113 4.4 18.5 1.0
SG L:CYS148 4.4 25.1 1.0
N L:PHE115 4.4 17.1 1.0
N L:ARG149 4.6 20.1 1.0
C L:GLN112 4.7 20.0 1.0
SG L:CYS116 4.7 21.4 1.0
CA L:GLY114 4.8 16.9 1.0
CB L:GLN112 4.9 19.4 1.0
N L:GLN112 4.9 19.6 1.0
C L:ARG149 5.0 18.9 1.0

Iron binding site 6 out of 8 in 3etr

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Iron binding site 6 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe601

b:22.4
occ:1.00
 FE2 L:FES601 0.0 22.4 1.0
S1 L:FES601 2.2 23.1 1.0
S2 L:FES601 2.2 23.8 1.0
SG L:CYS116 2.3 21.4 1.0
SG L:CYS148 2.5 25.1 1.0
FE1 L:FES601 2.7 21.9 1.0
CB L:CYS148 3.3 22.0 1.0
CB L:CYS116 3.3 18.8 1.0
CA L:CYS148 3.7 21.8 1.0
N L:ARG149 4.1 20.1 1.0
N L:CYS116 4.1 17.5 1.0
O L:HOH621 4.2 25.2 1.0
C L:CYS148 4.3 21.4 1.0
CA L:CYS116 4.3 18.7 1.0
N L:CYS150 4.4 18.6 1.0
CB L:CYS150 4.5 20.0 1.0
CG2 L:THR151 4.6 23.5 1.0
SG L:CYS150 4.7 19.8 1.0
SG L:CYS113 4.8 21.2 1.0
O L:LEU147 4.8 20.7 1.0
C L:CYS116 4.9 18.6 1.0
N L:PHE115 4.9 17.1 1.0
N L:CYS148 5.0 21.7 1.0
N L:THR117 5.0 20.1 1.0

Iron binding site 7 out of 8 in 3etr

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Iron binding site 7 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe602

b:21.0
occ:1.00
 FE1 L:FES602 0.0 21.0 1.0
S1 L:FES602 2.2 24.1 1.0
SG L:CYS51 2.2 21.8 1.0
S2 L:FES602 2.2 20.6 1.0
SG L:CYS73 2.3 19.3 1.0
FE2 L:FES602 2.9 19.8 1.0
CB L:CYS73 3.2 20.9 1.0
CB L:CYS51 3.5 19.9 1.0
N L:GLY46 4.2 23.4 1.0
N L:CYS73 4.2 21.4 1.0
CB L:ASN71 4.2 21.4 1.0
SG L:CYS43 4.3 19.2 1.0
CA L:CYS73 4.3 21.5 1.0
CG L:ASN71 4.4 22.6 1.0
N L:CYS51 4.4 18.6 1.0
OD1 L:ASN71 4.4 24.2 1.0
CA L:GLY46 4.5 23.9 1.0
CA L:CYS51 4.5 19.9 1.0
N L:GLY44 4.6 20.3 1.0
SG L:CYS48 4.6 17.1 1.0
CA L:GLY44 4.8 20.4 1.0
CA L:ASN71 4.9 22.9 1.0
N L:GLY49 4.9 17.6 1.0
N L:GLU45 4.9 22.2 1.0
ND2 L:ASN71 5.0 25.4 1.0

Iron binding site 8 out of 8 in 3etr

Go back to Iron Binding Sites List in 3etr
Iron binding site 8 out of 8 in the Crystal Structure of Xanthine Oxidase in Complex with Lumazine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Xanthine Oxidase in Complex with Lumazine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe602

b:19.8
occ:1.00
 FE2 L:FES602 0.0 19.8 1.0
SG L:CYS48 2.2 17.1 1.0
S2 L:FES602 2.2 20.6 1.0
S1 L:FES602 2.2 24.1 1.0
SG L:CYS43 2.2 19.2 1.0
FE1 L:FES602 2.9 21.0 1.0
N L:CYS43 3.4 18.3 1.0
CB L:CYS43 3.4 19.3 1.0
CB L:CYS48 3.4 19.3 1.0
N L:CYS48 3.6 21.7 1.0
N L:GLY49 3.9 17.6 1.0
CA L:CYS43 3.9 19.4 1.0
CA L:CYS48 3.9 18.6 1.0
C L:GLY42 4.0 18.9 1.0
N L:GLY44 4.1 20.3 1.0
C L:CYS48 4.2 17.8 1.0
N L:GLY46 4.3 23.4 1.0
CA L:GLY42 4.3 19.4 1.0
N L:GLY42 4.4 18.6 1.0
N L:GLY47 4.4 23.8 1.0
N L:ALA50 4.4 17.3 1.0
C L:CYS43 4.4 19.6 1.0
SG L:CYS73 4.5 19.3 1.0
SG L:CYS51 4.5 21.8 1.0
N L:GLU45 4.7 22.2 1.0
C L:GLY47 4.7 23.3 1.0
CA L:GLY46 4.8 23.9 1.0
C L:GLY46 4.8 24.4 1.0
O L:GLY42 4.8 18.7 1.0
CA L:GLY49 4.8 18.4 1.0
CB L:ALA50 5.0 17.9 1.0

Reference:

J.M.Pauff, H.Cao, R.Hille. Substrate Orientation and Catalysis at the Molybdenum Site in Xanthine Oxidase: Crystal Structures in Complex with Xanthine and Lumazine. J.Biol.Chem. V. 284 8760 2009.
ISSN: ISSN 0021-9258
PubMed: 19109252
DOI: 10.1074/JBC.M804517200
Page generated: Sun Aug 4 09:56:32 2024

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